If the WHO 2013 guidelines (initiation at 500 cells/μl and PMTCT option B+) were implemented in Ndhiwa, the proportion of HIV-positive individuals eligible for ART would rise from 60 to 82%.
The following settings were used for PhyML (implemented in Geneious 7.1.7): Estimated proportion of variable sites, optimization of topology/length/rate, best topology of NNI and SPR searches.
In model 8, the most stringent model implemented in PAML, a small proportion of codons (0.968%, 1.720%, and 2.207%) were estimated to be under selection, with ω values of 2.077, 16.110, and 1.529 for the ACE, REN, and SLC14A2 genes, respectively.
We conducted a Principal Coordinate Analysis (using NTSYS) based on NST indices, and an AMOVA of haplotype frequencies, implemented in Arlequin, to assess the proportion of genetic variance found at the region (North America vs. Europe), population and individual levels.
Statistical analysis included Chi-square, Fisher's exact test and proportion tests implemented in the software Epicalc (Brixton Health).
The Bayesian approach as implemented in MrBayes to detect the proportion of sites under different types of selection, after 200,000 MCMC generations, resulted in the following proportions (values between parentheses indicate the results of another, independent run): 76.0 % (76.9 %) negatively selected sites, 22.7 % (21.7 %) neutrally evolving sites, and 1.3 % (1.3 %) positively selected sites.
Comparison of binomial population proportions analysis implemented in Statlets (NWP Associates, Inc.; www.mrs.umn.edu/~sungurea/statlets/statlets.htm) indicates that the null hypothesis that the 2 proportions are equal could be rejected at significance level of 5.0%.
The difference in GC-content between the CRISPR- cas locus and the genome average was determined using a two-proportion test implemented in Minitab 17 (www.minitab.com).
Unlike most LAI algorithms, the global ancestry proportion estimation algorithm implemented in the software program ADMIXTURE assumes independent observations.
In this article, we use the allele-frequency admixture model implemented in Structure to infer the admixing proportions for individuals, and apply k-means clustering (Hartigan, 1975) on the estimated admixing proportions to learn the population label for each individual.
